This one's been my favorite since they posted it... I just can't help but, laugh. I know it's sick and twisted and it's horribly wrong but I can't help it.
My favorite one that I can probably think of is the one where the US army has a Dialga, but I'm too lazy to find it, so I'm using the first one that I laugh at going backwards.
The one that got them in trouble with American Greetings by imagining American McGee's version of Strawberry Shortcake. (It had to be pulled from the website.)
This isn't the funniest comic they've done but it's still one of my favorites. It came out around the time I grew annoyed with playing Star Wars Galaxies and started enjoying WoW. Being a jaded ex-SWG plater, now WoW fanatic, this holds a special place in my heart.